Hi,
I did already some investigation regarding the replay gain function of M0. I am using Foobar2000 for replay gain analysis.
M0 is not able to read replay gain info from cue sheets. M0 is able to read replay gain info only from tags. Foobar2000 stores replay gain info in embedded cue sheets (if they are present). This is probably why you have issue with replay gain function on your flac files.
I have not found a way how to make Foobar2000 store replay gain info in tags when an embedded cue sheet is present. I have found a workaround - to remove embedded cue sheet from the file, analyze it using the replay gain analyzer, store replay gain info, which now gets written in the tag since embedded cue sheet is not there, and then embed the cue sheet again. Then replay gain works even for flac with cue sheets in M0.
For flac without cue sheets replay gain works just fine (where album is split into songs/files).
With mp3, replay gain works mostly fine. I have stumbled upon several files, where replay gain info is nor read and applied by M0 even though the info is there and works normally in Foobar2000.